At that commemorative service, Warren again avoided controversy and borrowed a theme from the civil rights movement, "We Shall Overcome."
Over the weekend, about 100 gay rights supporters had marched and waved rainbow flags outside Warren's church in Lake Forest, Calif.
Problematic preachers like Warren have woven through the political life of Barack Obama, like a coat of many colors, all the way up to his inauguration as the 44th U.S. president.
First, firebrand Rev. Jeremiah Wright nearly derailed Obama's fight for the Democratic nomination. The uproar over his remarks from the pulpit such as "God damn America" and the U.S. being to blame for 9/11, prompted Obama to turn away from his former pastor and give a key speech on race and religion.
Then, the president-elect, who is a Christian, touched off a firestorm of controversy with Warren's selection.
As if to open the big tent even more, Obama picked V. Gene Robinson, the openly gay Anglican bishop from New Hampshire, to give the invocation at the start of inaugural events at the Lincoln Memorial on Sunday. Robinson had previously called Obama's choice of Warren a "slap in the face."
Gay rights advocates fumed over remarks Warren made to Beliefnet in December suggesting that if gay marriage were legal, why not incest, polygamy or "an older guy marrying a child?"
Conservative evangelicals were equally critical of Warren for accepting the inaugural invitation because of Obama's pro-choice abortion stance, just as they were when the president-elect joined a 2008 forum at Saddleback during the campaign.
But religious and even gay leaders are guardedly hopeful that this drama is yet another signal that Obama intends to rely on Lincoln's "team of rivals" approach to hear all points of view.
In the days before the inauguration, both preachers softened. When Robinson was named, Warren gushed to the New York Times that the president-elect had "again demonstrated his genuine commitment to bringing all Americans of goodwill together in search of common ground."
"I applaud his desire to be the president of every citizen," said Warren.
And Robinson echoed just last week, "Frankly, I think it is a magnificent, symbolic statement that Rick Warren and I will be praying for the new president and the nation. I think that's fantastic."
Gay activists say it is "heartening" to know that Robinson was included in the inaugural festivities, though his prayer wasn't televised in the live HBO special. But they were still uneasy about Warren's invocation, knowing the "symbolism" and "high profile" of that role.
"We are cautiously optimistic," said Joe Solmonese, president of the Human Rights Campaign, the nation's largest gay-rights group. Ultimately, he said, Obama is a friend of the lesbian, gay, bisexual, transgender community.
"The idea is that there is a place at the table for everybody, but at some point we draw the line, when you bring in people with incendiary views that say derogatory things about some Americans," he told ABCNews.com.
Some believe that Warren's centrist views -- supporting a broader agenda for evangelicals than just hot-button issues such as abortion and homosexuality -- might shift him to closer association with Obama.
Unlike ideologues like Jerry Falwell or Pat Robertson, Warren has talked about a loving Jesus, taking on causes like climate change, third-world poverty, sex trafficking and HIV/AIDS.